2. Alpha diversity: Shannon’s diversity index

  1. For the adult population.

  2. P-value is obtained by Wilcoxon Rank Sum Test for alpha diversities.

2.1 Main figures

2.2 Supplementary figures

3. Beta diversity: Bray-Curtis dissimilarity

  1. For the adult population.

  2. P-values are obtained by Permutational Multivariate Analysis of Variance (PERMANOVA) and Permutational Analysis of Multivariate Dispersion (PERMDISP) for beta diversities.

3.1 Main figures

quartz_off_screen 
                2 
quartz_off_screen 
                2 

3.2 Supplementary figures

Session information

R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggpubr_0.4.0       qwraps2_0.5.2      magrittr_2.0.1     compositions_2.0-2
 [5] vegan_2.5-7        lattice_0.20-44    permute_0.9-5      microbiome_1.14.0 
 [9] phyloseq_1.36.0    forcats_0.5.1      stringr_1.4.0      dplyr_1.0.7       
[13] purrr_0.3.4        tidyr_1.1.3        tibble_3.1.4       ggplot2_3.3.5     
[17] tidyverse_1.3.1    openxlsx_4.2.4     readr_2.0.1       

loaded via a namespace (and not attached):
  [1] Rtsne_0.15             colorspace_2.0-2       ggsignif_0.6.3        
  [4] rio_0.5.27             ellipsis_0.3.2         XVector_0.32.0        
  [7] fs_1.5.0               rstudioapi_0.13        farver_2.1.0          
 [10] bit64_4.0.5            fansi_0.5.0            lubridate_1.7.10      
 [13] xml2_1.3.2             codetools_0.2-18       splines_4.1.1         
 [16] robustbase_0.93-8      knitr_1.34             ade4_1.7-18           
 [19] jsonlite_1.7.2         broom_0.7.9            cluster_2.1.2         
 [22] dbplyr_2.1.1           compiler_4.1.1         httr_1.4.2            
 [25] backports_1.2.1        assertthat_0.2.1       Matrix_1.3-4          
 [28] fastmap_1.1.0          cli_3.0.1              htmltools_0.5.2       
 [31] tools_4.1.1            igraph_1.2.6           gtable_0.3.0          
 [34] glue_1.4.2             GenomeInfoDbData_1.2.6 reshape2_1.4.4        
 [37] Rcpp_1.0.7             carData_3.0-4          Biobase_2.52.0        
 [40] cellranger_1.1.0       jquerylib_0.1.4        vctrs_0.3.8           
 [43] Biostrings_2.60.2      rhdf5filters_1.4.0     multtest_2.48.0       
 [46] ape_5.5                nlme_3.1-153           iterators_1.0.13      
 [49] tensorA_0.36.2         xfun_0.26              rvest_1.0.1           
 [52] lifecycle_1.0.0        rstatix_0.7.0          DEoptimR_1.0-9        
 [55] zlibbioc_1.38.0        MASS_7.3-54            scales_1.1.1          
 [58] vroom_1.5.5            hms_1.1.0              parallel_4.1.1        
 [61] biomformat_1.20.0      rhdf5_2.36.0           RColorBrewer_1.1-2    
 [64] curl_4.3.2             yaml_2.2.1             gridExtra_2.3         
 [67] stringi_1.7.4          highr_0.9              S4Vectors_0.30.0      
 [70] foreach_1.5.1          BiocGenerics_0.38.0    zip_2.2.0             
 [73] GenomeInfoDb_1.28.4    rlang_0.4.11           pkgconfig_2.0.3       
 [76] bitops_1.0-7           evaluate_0.14          Rhdf5lib_1.14.2       
 [79] labeling_0.4.2         cowplot_1.1.1          bit_4.0.4             
 [82] tidyselect_1.1.1       plyr_1.8.6             R6_2.5.1              
 [85] IRanges_2.26.0         generics_0.1.0         DBI_1.1.1             
 [88] foreign_0.8-81         pillar_1.6.2           haven_2.4.3           
 [91] withr_2.4.2            mgcv_1.8-36            abind_1.4-5           
 [94] survival_3.2-13        RCurl_1.98-1.5         bayesm_3.1-4          
 [97] car_3.0-11             modelr_0.1.8           crayon_1.4.1          
[100] utf8_1.2.2             tzdb_0.1.2             rmarkdown_2.11        
[103] grid_4.1.1             readxl_1.3.1           data.table_1.14.0     
[106] reprex_2.0.1           digest_0.6.27          stats4_4.1.1          
[109] munsell_0.5.0